8,616 research outputs found
Evaluation of different segmentation-based approaches for skin disorders from dermoscopic images
Treballs Finals de Grau d'Enginyeria Biomèdica. Facultat de Medicina i Ciències de la Salut. Universitat de Barcelona. Curs: 2022-2023. Tutor/Director: Sala Llonch, Roser, Mata Miquel, Christian, Munuera, JosepSkin disorders are the most common type of cancer in the world and the incident has been lately increasing over the past decades. Even with the most complex and advanced technologies, current image acquisition systems do not permit a reliable identification of the skin lesion by visual examination due to the challenging structure of the malignancy. This promotes the need for the implementation of automatic skin lesion segmentation methods in order to assist in physicians’ diagnostic when determining the lesion's region and to serve as a preliminary step for the classification of the skin lesion. Accurate and precise segmentation is crucial for a rigorous screening and monitoring of the disease's progression.
For the purpose of the commented concern, the present project aims to accomplish a state-of-the-art review about the most predominant conventional segmentation models for skin lesion segmentation, alongside with a market analysis examination. With the rise of automatic segmentation tools, a wide number of algorithms are currently being used, but many are the drawbacks when employing them for dermatological disorders due to the high-level presence of artefacts in the image acquired.
In light of the above, three segmentation techniques have been selected for the completion of the work: level set method, an algorithm combining GrabCut and k-means methods and an intensity automatic algorithm developed by Hospital Sant Joan de Déu de Barcelona research group. In addition, a validation of their performance is conducted for a further implementation of them in clinical training. The proposals, together with the got outcomes, have been accomplished by means of a publicly available skin lesion image database
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Production networks in the cultural and creative sector: case studies from the publishing industry
The CICERONE project investigates cultural and creative industries through case study research, with a focus on production networks. This report, part of WP2, examines the publishing industry within this framework. It aims to understand the industry’s hidden aspects, address statistical issues in measurement, and explore the industry’s transformation and integration of cultural and economic values. The report provides an overview of the production network, explores statistical challenges, and presents qualitative analyses of two case studies. It concludes by highlighting the potential of the Global Production Network (GPN) approach for analyzing, researching, policymaking, and intervening in the European publishing network.
The CICERONE project’s case study research delves into the publishing industry, investigating its production networks and examining key aspects often unseen by the public. The report addresses statistical challenges in measuring the industry and sheds light on its ongoing transformations and integration of cultural and economic values. It presents an overview of the production network, explores statistical issues, and provides qualitative analyses of two case studies. The report emphasizes the potential of the GPN approach for analyzing and intervening in the European publishing network, ultimately contributing to research, policymaking, and understanding within the industry
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Ensuring Access to Safe and Nutritious Food for All Through the Transformation of Food Systems
Estudo da remodelagem reversa miocárdica através da análise proteómica do miocárdio e do líquido pericárdico
Valve replacement remains as the standard therapeutic option for aortic
stenosis patients, aiming at abolishing pressure overload and triggering
myocardial reverse remodeling. However, despite the instant hemodynamic
benefit, not all patients show complete regression of myocardial hypertrophy,
being at higher risk for adverse outcomes, such as heart failure. The current
comprehension of the biological mechanisms underlying an incomplete reverse
remodeling is far from complete. Furthermore, definitive prognostic tools and
ancillary therapies to improve the outcome of the patients undergoing valve
replacement are missing. To help abridge these gaps, a combined myocardial
(phospho)proteomics and pericardial fluid proteomics approach was followed,
taking advantage of human biopsies and pericardial fluid collected during
surgery and whose origin anticipated a wealth of molecular information
contained therein.
From over 1800 and 750 proteins identified, respectively, in the myocardium
and in the pericardial fluid of aortic stenosis patients, a total of 90 dysregulated
proteins were detected. Gene annotation and pathway enrichment analyses,
together with discriminant analysis, are compatible with a scenario of increased
pro-hypertrophic gene expression and protein synthesis, defective ubiquitinproteasome system activity, proclivity to cell death (potentially fed by
complement activity and other extrinsic factors, such as death receptor
activators), acute-phase response, immune system activation and fibrosis.
Specific validation of some targets through immunoblot techniques and
correlation with clinical data pointed to complement C3 β chain, Muscle Ring
Finger protein 1 (MuRF1) and the dual-specificity Tyr-phosphorylation
regulated kinase 1A (DYRK1A) as potential markers of an incomplete
response. In addition, kinase prediction from phosphoproteome data suggests
that the modulation of casein kinase 2, the family of IκB kinases, glycogen
synthase kinase 3 and DYRK1A may help improve the outcome of patients
undergoing valve replacement. Particularly, functional studies with DYRK1A+/-
cardiomyocytes show that this kinase may be an important target to treat
cardiac dysfunction, provided that mutant cells presented a different response
to stretch and reduced ability to develop force (active tension).
This study opens many avenues in post-aortic valve replacement reverse
remodeling research. In the future, gain-of-function and/or loss-of-function
studies with isolated cardiomyocytes or with animal models of aortic bandingdebanding will help disclose the efficacy of targeting the surrogate therapeutic
targets. Besides, clinical studies in larger cohorts will bring definitive proof of
complement C3, MuRF1 and DYRK1A prognostic value.A substituição da válvula aórtica continua a ser a opção terapêutica de
referência para doentes com estenose aórtica e visa a eliminação da
sobrecarga de pressão, desencadeando a remodelagem reversa miocárdica.
Contudo, apesar do benefício hemodinâmico imediato, nem todos os pacientes
apresentam regressão completa da hipertrofia do miocárdio, ficando com maior
risco de eventos adversos, como a insuficiência cardíaca. Atualmente, os
mecanismos biológicos subjacentes a uma remodelagem reversa incompleta
ainda não são claros. Além disso, não dispomos de ferramentas de
prognóstico definitivos nem de terapias auxiliares para melhorar a condição
dos pacientes indicados para substituição da válvula. Para ajudar a resolver
estas lacunas, uma abordagem combinada de (fosfo)proteómica e proteómica
para a caracterização, respetivamente, do miocárdio e do líquido pericárdico
foi seguida, tomando partido de biópsias e líquidos pericárdicos recolhidos em
ambiente cirúrgico.
Das mais de 1800 e 750 proteínas identificadas, respetivamente, no miocárdio
e no líquido pericárdico dos pacientes com estenose aórtica, um total de 90
proteínas desreguladas foram detetadas. As análises de anotação de genes,
de enriquecimento de vias celulares e discriminativa corroboram um cenário de
aumento da expressão de genes pro-hipertróficos e de síntese proteica, um
sistema ubiquitina-proteassoma ineficiente, uma tendência para morte celular
(potencialmente acelerada pela atividade do complemento e por outros fatores
extrínsecos que ativam death receptors), com ativação da resposta de fase
aguda e do sistema imune, assim como da fibrose.
A validação de alguns alvos específicos através de immunoblot e correlação
com dados clínicos apontou para a cadeia β do complemento C3, a Muscle
Ring Finger protein 1 (MuRF1) e a dual-specificity Tyr-phosphoylation
regulated kinase 1A (DYRK1A) como potenciais marcadores de uma resposta
incompleta. Por outro lado, a predição de cinases a partir do fosfoproteoma,
sugere que a modulação da caseína cinase 2, a família de cinases do IκB, a
glicogénio sintase cinase 3 e da DYRK1A pode ajudar a melhorar a condição
dos pacientes indicados para intervenção. Em particular, a avaliação funcional
de cardiomiócitos DYRK1A+/- mostraram que esta cinase pode ser um alvo
importante para tratar a disfunção cardíaca, uma vez que os miócitos mutantes
responderam de forma diferente ao estiramento e mostraram uma menor
capacidade para desenvolver força (tensão ativa).
Este estudo levanta várias hipóteses na investigação da remodelagem reversa.
No futuro, estudos de ganho e/ou perda de função realizados em
cardiomiócitos isolados ou em modelos animais de banding-debanding da
aorta ajudarão a testar a eficácia de modular os potenciais alvos terapêuticos
encontrados. Além disso, estudos clínicos em coortes de maior dimensão
trarão conclusões definitivas quanto ao valor de prognóstico do complemento
C3, MuRF1 e DYRK1A.Programa Doutoral em Biomedicin
Increased lifetime of Organic Photovoltaics (OPVs) and the impact of degradation, efficiency and costs in the LCOE of Emerging PVs
Emerging photovoltaic (PV) technologies such as organic photovoltaics (OPVs) and perovskites (PVKs) have the potential to disrupt the PV market due to their ease of fabrication (compatible with cheap roll-to-roll processing) and installation, as well as their significant efficiency improvements in recent years. However, rapid degradation is still an issue present in many emerging PVs, which must be addressed to enable their commercialisation. This thesis shows an OPV lifetime enhancing technique by adding the insulating polymer PMMA to the active layer, and a novel model for quantifying the impact of degradation (alongside efficiency and cost) upon levelized cost of energy (LCOE) in real world emerging PV installations.
The effect of PMMA morphology on the success of a ternary strategy was investigated, leading to device design guidelines. It was found that either increasing the weight percent (wt%) or molecular weight (MW) of PMMA resulted in an increase in the volume of PMMA-rich islands, which provided the OPV protection against water and oxygen ingress. It was also found that adding PMMA can be effective in enhancing the lifetime of different active material combinations, although not to the same extent, and that processing additives can have a negative impact in the devices lifetime.
A novel model was developed taking into account realistic degradation profile sourced from a literature review of state-of-the-art OPV and PVK devices. It was found that optimal strategies to improve LCOE depend on the present characteristics of a device, and that panels with a good balance of efficiency and degradation were better than panels with higher efficiency but higher degradation as well. Further, it was found that low-cost locations were more favoured from reductions in the degradation rate and module cost, whilst high-cost locations were more benefited from improvements in initial efficiency, lower discount rates and reductions in install costs
Fifth-Dimensional Warfare and National Security in Canada: Situating Microdeviation Theory Within C-59: An Act Respecting National Security Matters
In an era of rapid technological change, the growing threat environment in the cyber dimension will continue to influence how a sovereign nation contends with attacks that can occur from any corner of the world. The growing adaptation and expansion of technology belonging to the Internet of Things (IoT) and the increasing prevalence of social media (Facebook, Twitter) has also influenced the spreading of attack surfaces that can become victim to exploitation by motivated parties including foreign states and terrorist groups. Against this backdrop, Canada’s own efforts to modernize and reinforce its own national security agencies resulted in the developing and royal assent of 2017’s Bill C-59: An Act Respecting National Security Matters. The royal assent of C-59 poses a unique opportunity to examine the underlying narratives and evidence used by expert witnesses and committee members alike to frame the threat that the cyber environment has when influencing C-59’s more controversial measures. This includes the expansion of the Communication Security Establishment’s (CSE) traditional 3-part mandate to include the use of cyberoperations, or the expansion of Canada’s nation security agencies to utilize the loosely defined “public datasets” despite concerns of possible misappropriation. Utilizing Popham’s (2018) Theory of Microdeviation, this thesis highlights the normalized experiences of Canadians online when considering the exploitation of IoT technology and social media to conduct attacks or sabotage against democratic states, and how these narratives were often used to advance C59’s modernization push. Finally, this thesis also analyzes the implications of C-59 when considering the international community as it relates to a growing cyber arms race akin to 20th century Cold War fears, and how Microdeviation Theory has utility when examining the goals of legislation seeking to control deviant behaviour online
Elasto-plastic deformations within a material point framework on modern GPU architectures
Plastic strain localization is an important process on Earth. It strongly influ- ences the mechanical behaviour of natural processes, such as fault mechanics, earthquakes or orogeny. At a smaller scale, a landslide is a fantastic example of elasto-plastic deformations. Such behaviour spans from pre-failure mech- anisms to post-failure propagation of the unstable material. To fully resolve the landslide mechanics, the selected numerical methods should be able to efficiently address a wide range of deformation magnitudes.
Accurate and performant numerical modelling requires important compu- tational resources. Mesh-free numerical methods such as the material point method (MPM) or the smoothed-particle hydrodynamics (SPH) are particu- larly computationally expensive, when compared with mesh-based methods, such as the finite element method (FEM) or the finite difference method (FDM). Still, mesh-free methods are particularly well-suited to numerical problems involving large elasto-plastic deformations. But, the computational efficiency of these methods should be first improved in order to tackle complex three-dimensional problems, i.e., landslides.
As such, this research work attempts to alleviate the computational cost of the material point method by using the most recent graphics processing unit (GPU) architectures available. GPUs are many-core processors originally designed to refresh screen pixels (e.g., for computer games) independently. This allows GPUs to delivers a massive parallelism when compared to central processing units (CPUs).
To do so, this research work first investigates code prototyping in a high- level language, e.g., MATLAB. This allows to implement vectorized algorithms and benchmark numerical results of two-dimensional analysis with analytical solutions and/or experimental results in an affordable amount of time. After- wards, low-level language such as CUDA C is used to efficiently implement a GPU-based solver, i.e., ep2-3De v1.0, can resolve three-dimensional prob- lems in a decent amount of time. This part takes advantages of the massive parallelism of modern GPU architectures. In addition, a first attempt of GPU parallel computing, i.e., multi-GPU codes, is performed to increase even more the performance and to address the on-chip memory limitation. Finally, this GPU-based solver is used to investigate three-dimensional granular collapses and is compared with experimental evidences obtained in the laboratory.
This research work demonstrates that the material point method is well suited to resolve small to large elasto-plastic deformations. Moreover, the computational efficiency of the method can be dramatically increased using modern GPU architectures. These allow fast, performant and accurate three- dimensional modelling of landslides, provided that the on-chip memory limi- tation is alleviated with an appropriate parallel strategy
Fine-scale changes in flight effort revealed by animal-borne loggers
The movements of the air are central to the life of flying birds, because they can determine whether the costs of flight are closer to resting or sprinting, and whether birds are able to reach their destination. Yet for species relying mainly on flapping flight, studies about the effects of weather on flight effort have mainly focussed on wind, with other atmospheric factors receiving less attention. In addition, with the development of new technologies to measure flight effort, it has become clear that some methods need standardisation and further verification. The goal of this PhD is to provide insight into how atmospheric conditions affect flight costs more broadly and study the extent to which birds prioritise energy expenditure over other currencies, such as time and risk. I used high-frequency data-loggers to explore the combined effects of wind and thermals, as well as air density, on flight effort over fine scales, as well as how birds adjust their behaviour to these factors. Results showed that pigeons (Columba livia), which are not limited by energy expenditure, prioritise speed over energy savings, and use a very costly flight style which could serve as a predator-avoidance strategy. I also found that wind support was a strong predictor of whether chick-rearing tropicbirds (Phaethon rubricauda) use thermal soaring to save energy during foraging trips, suggesting that birds were weighing up the trade-off between energy and time, and chose to save energy only when this would not cost them too much time. Comparison of air density between seasons also revealed that the flapping flight of tropicbirds was more costly during summer, when air density was lower. This finding shows that the effect of seasonal changes in air density on flight costs is significant, outweighing the influence of both wind and thermal availability. It also sheds new light on how flight costs (particularly those in tropical birds) might be affected by global change. Finally, the analysis of the accelerometer data showed that the type of tag used, as well as differences in the longitudinal position and attachment method, affected the amplitude of the signal, which has implications for the robustness of acceleration-based proxies for flight effort. Nonetheless, the adoption of standardized calibrations should facilitate the comparison of these metrics between study sites and through time, improving the prospect that they can be used to study the effect of a changing climate on flight costs and avian ecology
Role of STIL overexpression in supernumerary centriole formation, chromosomal instability and cancer development in mice
Centrosome is the major microtubule-organizing center in mammalian cell and consists of a pair of centrioles embedded in pericentriolar material. Centrosomes are important for bipolar spindle formation and correct chromosome segregation during mitosis. Disruption of normal centrosome function leads to aneuploidy and chromosome missegregation. Many cancer cells harbor supernumerary centrosomes, which were shown to correlate to chromosomal instability, clinical aggressiveness, and poor prognosis. Nevertheless, the question, whether amplified centrosomes can drive tumorigenesis in vivo remains unresolved.
The process of centrosome duplication is tightly controlled by a small set of proteins including the kinase protein PLK4 and the structural centriole proteins as STIL and SAS6. Depletion of any one of these proteins’ blocks centrosome duplication and, conversely, overexpression causes centrosome amplification. In different PLK4 overexpression in vivo models, it remains arguable, whether extra centrosomes could derive tumorigenesis and whether the generated tumors might be induced by the additional serine/threonine kinase functions of PLK4 besides its role in regulating centriole duplication.
On the other hand, the structural centrosome protein STIL is involved only in centriole replication without any other known functions up to now and its overexpression leads to the formation of supernumerary centrioles in tissue culture. Therefore, investigating the role of centrosome aberrations in chromosomal instability and tumor formation in vivo using STIL overexpression (STILOE) mouse model will add important information to the conflicting data generated by PLK4 overexpressing mice.
Accordingly, we generated a new transgenic Cre-LoxP mouse model, B6-STIL, that overexpresses STIL when bred with a Cre-deleter line leading to STOP cassette excision. These mice were used for (i) generation and characterization of mice with ubiquitous STIL overexpression (STILOE) for the assessment of spontaneous centrosome amplification-driven tumor development; (ii) generation and characterization of mouse embryonic fibroblasts (MEFs) derived from these STILOE mice to determine STIL overexpression levels and the development of centrosome amplification, mitotic aberrations; (iii) generation and characterization of mice with tamoxifen-inducible epithelium-specific STIL overexpression (K14(CreERT2);STILOE) with and without active TP53, which were used in skin carcinogenesis assays, to determine the relative contribution of supernumerary centrosomes and chromosomal instability to chemical tumor induction and progression.
Our results showed a graded overexpression of STIL mRNA and protein in early MEFs passages and tissues from heterozygous STILOE and homozygous STILOE mice, leading to significant centrosome amplification and chromosomal aberrations via aberrant mitoses. Importantly, MEFs with high levels of STIL-induced centrosome amplification showed a proliferative disadvantage with a strong selective pressure to eliminate cells overexpressing STIL by apoptosis and senescence. In line, rates of both, spontaneous tumor formation in STILOE mice and chemically induced skin tumors in K14(CreERT2);STILOE animals are largely reduced as compared to controls. Thus, centrosome amplification induced by STIL overexpression seems to inhibit tumor formation rather than enhancing it in vivo in mammals
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